Plunged Into Darkness
by Dead Man's Toe
Summary: When Clara and Molly are kidnapped, John calls the Doctor for help finding them. Sherlock hears of this and decides that his hiatus is over. (Sequel to Murder and Aliens) (Rated for violence).
1. Prologue: Post Reichenbach

It had been about a year and a half since Sherlock had fallen, and John still avoided Baker Street. Within a few weeks after the incident, he had moved in with his girlfriend, Clara Oswald. She had been the kindest girlfriend he could ever have hoped for.

Upon seeing his grief, Clara had demanded that the Doctor try to bring Sherlock back. Somehow, he had managed to steer the TARDIS into Hell. Though they tried, they couldn't find him there.

Then, the Cybermen rose from the ground, and the Mistress revealed herself. While she and the Doctor were on some sort of ship, Clara found herself standing in a graveyard surrounded by zombie Cybermen. Danny Pink, who had been hit by a car just a week prior, tracked her down and confessed that deep down, he still loved her and always would.

The rest, everybody knows. Danny Pink destroyed the Cybermen, and the Doctor killed the Mistress.

Clara returned to John that night and told him what she had tried to do, and how she had failed. They held each other close, missing their friend and wondering for the millionth time why he had jumped.

Months passed, and the Doctor never stopped by again. Clara told John that he had gone home, and John wondered what could be more like home than dinner at Angelo's with Clara, Sherlock, Molly, and the Doctor.

Then, there was the Christmas when Clara almost didn't wake up. The Doctor came around more frequently after that, and John went with him and Clara.

As time passed, the ache of losing Sherlock lessened, but it was never fully gone. As he walked home, he took great care to avoid Baker Street. It was just too painful to walk down. He would give anything just to have his best friend back.

He approached the door to the flat and paused. It had been thrown open violently. He ran inside, shouting Clara's name. There was no trace of her anywhere. John began to panic as he tore the place apart.

Clara's phone had been flung to the floor. With trembling hands, John picked it up and began to search through her contacts. He found the Doctor's name and dialed.

"Clara? How can I help you?"

"It's John. I need your help. Clara's gone missing. I think she was taken."

* * *

><p><strong>AN: <strong>Sorry if this feels rushed. I wanted to explain how those events fit in here without rewriting the shows. This prologue is mainly just set up for the story. Next chapter will be back to normal.


	2. Taken

**AN: **I do not own Sherlock or Doctor Who, though I'm sure you already knew that. I guess I've been in a writing mood today, but I really wanted to get a real chapter put up.

* * *

><p>A few minutes after John hung up the phone, he could hear the all too familiar sound of the TARDIS landing in his living room. Normally, the noise filled John with eager excitement, but today, it filled him with dreading anticipation.<p>

The Doctor rushed out of the TARDIS with his sonic screwdriver held in front of him. He immediately began scanning the room for any trace of Clara's kidnapper. His face was drawn tight with worry and only became tighter as the Doctor's search became more frantic.

"These readings are definitely alien," he finally said. "It's odd, though. For some reason, they're really stale looking."

"Can you find her?" John asked, fearing the answer. "I can't lose anyone else."

"I'll find her," the Doctor promised. "Even if I have to go to Hell, which I already have."

"I called the police," John added. "Doctor, Molly is missing too."

The Doctor stopped his panicked searching and froze. "What if the same thing took her?" he asked.

"It's worth checking out," John agreed.

The Doctor opened the TARDIS door with a snap of his fingers and hurried inside. John followed, taking a brief moment to look back on the mess of a flat he was leaving. He wondered how long it would be before he returned, and if he would be returning alone or with Clara.

He shook his head to clear his worrying and stepped inside. The door shut quickly behind him. It was as if the TARDIS had picked up on the urgency of the situation. Knowing her, she probably had. She was very smart and extremely perceptive.

As the TARDIS flew into the vortex, John's mind wandered to the first time he had set foot in the TARDIS. Clara had been with him then, and so had Sherlock. Despite the fact that he was chasing a homicidal alien, he had been much happier then.

The TARDIS shook as she landed in Molly's flat. John and the Doctor wasted no time in exiting and searching the place over. The Doctor's sonic whirred, but judging by his facial expression, he was having about as much luck as he had back at John and Clara's flat.

"Same?" John asked.

"Same," the Doctor confirmed.

John groaned and sat down on Molly's couch. A million scenarios raced through his mind, each more gruesome than the last. He couldn't help but picture Clara dead with a monstrous alien standing over her.

"John," the Doctor called, pulling him out of his morbid thoughts. "We will find them."

"I know," he replied, doing his best to sound confident. "What do we do first?"

"We consult UNIT," the Doctor decided. Placing the screwdriver back in his pocket, he bounded back to the TARDIS.

The Doctor was trying to sound confident as well, but John could hear the subtle nervousness in his voice. Clara was his best friend, and John knew as well as anyone how terrifying losing your best friend was. With a sigh, he followed the Doctor back inside the TARDIS.

"Weren't you impersonating UNIT when we first met?" John asked. The memories of that day that assaulted him hurt, causing him to cringe involuntarily.

"Yes," the Doctor answered. "Don't worry, they won't mind. They love me. In fact, they even made me President of the Earth temporarily."

Despite the grim situation, John chuckled. "When was that?"

"The day the Cybermen rose from the ground."

John shook his head and marveled at the strange life he led. With all that he had lost, he started to wonder if it was worth it. He quickly reminded himself that it had brought him Sherlock and Clara, and even if it was only for a short time, it was always worth it.

The TARDIS shook as she landed. John followed the Doctor through the TARDIS door once more into what appeared to be someone's office. Two women on either side of a desk were staring at them in shock. "Doctor?" the one behind the desk asked. "What brings you here?"

"It's really you," the other one gasped in amazement. "You look different."

"This is my friend, John Watson," the Doctor introduced. "John, meet Chief Scientific Officer Kate Stewart and Dr. Martha Smith. We need your help."

* * *

><p>As Sherlock stretched and groaned, he wondered if he looked as awful as he felt. Moriarty's network was more extensive than he had ever imagined, and destroying it was starting to be exhausting. Every muscle ached, and he longed to go back home to John and Molly.<p>

An old cut on his arm had opened up again and was bleeding all over the hotel sink. One of Mycroft's men had stitched it up, but not very well apparently. Sherlock gently cleaned it with a threadbare rag and cursed his life.

What I wouldn't give to go to the Sisters of the Infinite Schism, Sherlock grumbled to himself. This job was the most dangerous he had ever had, and he was covered in injuries. He remembered how the doctors there had completely healed John's broken arm in mere hours. Sherlock's wrist was still sore from where it had been broken months ago, and he was getting impatient with it.

Cursing his life once again, Sherlock collapsed onto the bed. The springs squeaked loudly underneath him. Sherlock sighed as he buried his face into the tiny pillow. Mycroft couldn't even book him a nice hotel most days, despite all his money.

Sherlock's phone rang, and he groaned before digging it out of his pocket. "What is it Mycroft?" he grumbled.

"I'm on a private jet to collect you," his brother answered.

"I'm not done here yet," Sherlock protested.

"I'll send someone else in to finish it up," Mycroft assured him.

"Fine," Sherlock sighed. "Where am I due next?"

"London," Mycroft answered.

Sherlock sat straight up in the bed. Had he really heard that right? "I'm coming home?"

"Yes," his brother replied. "Something's come up. I'll explain in a minute. Come to the field behind the hotel, where I dropped you off."

Mycroft hung up, and Sherlock thrust his phone back into his pocket as he jumped off the bed. He threw his clothes into his suitcase and ran out the door. He received a few odd looks as he ran down the hallway and stairs, but he wasn't paying much attention.

He paused at the desk to check out, and continued to run outside the building. He ran around the back of the building and saw Mycroft's jet waiting in the field. For the first time in a year and a half, a genuine smile broke out on his face.

He ran across the field, straight to the jet. Mycroft was waiting for him inside. Sherlock hurriedly sat across from him, still grinning. The grin vanished as soon as Sherlock looked at Mycroft's grim face. "What's wrong?" he demanded.

The jet took off towards home, but it was not as joyous as Sherlock had imagined it would be. His stomach was in knots as Mycroft searched for the right words.

"I know about the case you took with the Doctor," he began. "I know who he is. I've been monitoring UNIT for some time now."

Sherlock nodded, waiting for him to continue.

"I've been monitoring John as well, like you asked."

Sherlock's internal alarm screamed at him. "What happened? Is he alright?"

"Clara and Molly have gone missing, and John's gone off with the Doctor to find them. Sherlock, they were taken."

Sherlock's jaw dropped in shock, which is something that rarely happened. "Taken?" he finally asked. "By who?"

"That's what I'm hoping you can find out."


	3. The Dark Room

The dull throb in her skull was the first thing Clara Oswald noticed when she woke up.

She squeezed her eyes tight and pressed her fingers to her temples. The pain didn't subside. Clara pushed herself up into a sitting position on the mattress. When her head protested, she laid down again and curled into a tight ball.

The second thing she noticed was that she wasn't in her bed.

Normally, Clara would have realized that instantly, but the pain in her head dulled her senses. She struggled to remember how she got there, but the throbbing was too great. She could barely focus on anything else. Everything was a blur.

Clara forced her eyes open. She blinked a few times, dazed. Pitch black darkness completely surrounded her. She waved her hands in front of her face to confirm that she couldn't see anything.

Panic started to set in. Clara frantically felt around the mattress, looking for any clue to help her figure out where she was. Her hand struck a warm arm. "Doctor?" Clara asked hesitantly. Her voice was groggy, and she had trouble forcing the word out.

Clara moved her hand down to the other person's hand. It felt like a women's hand. She squeezed it tightly, afraid that it might disappear if she let go. "You 'wake?" she managed to ask.

The other women groaned. "Sh'lock?" she slurred. Clara's heart calmed as she recognized the voice.

"Molly?" she asked. "'ts me. Clara."

"Clara?" Molly groaned. The hand Clara held gripped back. "Where 'm I? Why'st dark?"

"C'n you 'member 'nything?" Clara slurred.

Molly only groaned in response, "Head hurts."

Clara forced herself into a kneeling position. The ache in her skull was starting to lesson. She gently felt Molly's forehead to check for fever, but the other girl felt normal. Clara laid down again. She let go of Molly's hand and pressed her back up against the pathologist's.

Memories of the previous night were starting to come back to her. She could remember being at home, waiting for John to return when someone broke down her door. Anything after that was fuzzy. Clara felt around her head, looking for sign of injury. She found nothing.

With relief, Clara decided that she was drugged, not concussed. Hopefully whatever was in her system would wear off soon. Then, she could try to find a way out. "You 'lright?" she asked.

"'m sc'red," Moly replied.

"Me too," Clara stated.

Molly pressed closer to Clara. The warmth of her friend was all Clara needed to keep calm. When she travelled with the Doctor, she ended up in situations like these more times than she cared to admit. However, this was the first time she was without the Doctor. It was also the first time she had been completely unable to see. Still, despite the extra difficulties, Clara was confident that she would find her way out.

"We'll be fine," Clara said reassuringly. "I promise I'll get us out of here." Though sleep still clung to her voice, talking was getting easier.

With her headache nearly gone, Clara pushed herself up and crawled to the wall. The mattress was in a corner. She felt her way along the wall, still crawling. She didn't have the energy to stand yet. Molly groaned at her absence, but Clara hardly registered it.

The floor was cold cement. It hurt Clara's knees to crawl over it, but she was determined to get her bearings and find out as much about the room as possible. As she continued, she kept one hand on the wall for reassurance, and the other felt the way in front of her.

She hit the next corner sooner than she expected. There had been nothing in her way. Clara turned, continuing to feel her path. She crawled a little ways before her hand came into contact with a large, steel door. Using it as support, Clara pushed herself to her feet. Her hands explored the door, looking for a knob or a window. Though she had hoped, she wasn't surprised when she found nothing.

"Clara?" Molly called out. "You still there?"

"I'm here," Clara answered. "I just thought I would map out the room."

"Good idea," Molly returned. Clara could hear her weight on the mattress shifting. After a second, the sound changed into Molly's hands hitting the cement floor.

Clara continued to slowly feel her way along the wall. Each footstep was cautious as she maneuvered to the next corner. Besides the door, there was nothing out of the ordinary along that wall.

"Clara?" Molly called out again, sounding panicked. "Where are you?"

"I'm at the opposite corner from the mattress. Where are you?"

"I don't know," Molly replied. Her voice rose a pitch in fear.

"Don't tell me you just crawled out into the darkness," Clara said.

"Yes," came the meek reply. "Clara, help me."

* * *

><p>Molly's breaths came in faster as she realized that she was lost in the darkness. She sat up and grabbed her shirt in her fists. She could feel waves of panic rushing through her as a stray tear streaked down her cheek. Somewhere in her mind, she knew that she needed to calm down, but her thoughts were too disorganized.<p>

"I can help you, Molly, but you need to calm down first."

"Okay," Molly responded. Her body was shaking, and her breathing only quickened. She clenched her fists tighter, but it didn't seem to help. Molly was spiraling fast into panic.

Through the darkness, Clara's voice broke through. It took Molly a few seconds to realize that the teacher was singing. Using all her willpower, Molly focused in on her voice. The calming effect was almost instantaneous.

"Okay," Molly repeated. Her heart was still pounding, but she was in control of her body again. "What do I do now?"

"Can you crawl towards the sound of my voice? The room isn't very big."

"Alright," Molly agreed. She turned to face where she thought Clara was standing and started to crawl. "Keep talking."

"As soon as we get out of here, I'm going to personally kill each alien that's keeping us here."

Molly's hand came into contact with a foot. "Clara?" she asked.

The person in front of her knelt down and took her hand. "Yes," Clara answered. "It's me."

Relief coursed through Molly as he clung tightly onto the hand. With Clara's help, she stood up and brought her other hand to the wall. The two women held to each other as they made their way across the room. "You really think this is aliens?" Molly asked.

"Who else could it be?" Clara responded.

Eventually, the pair made it back to the mattress. They collapsed onto it with great relief. It seemed to be the only thing in the dark room. Like before, Clara and Molly pressed their backs to one another.

Clara's confidence comforted Molly as her eyes drooped. She had to believe that they would get out, or she would lose all hope. Her exhaustion claimed her, and Molly fell into a deep sleep.


	4. Straws

As Martha looked into the Doctor's eyes, he couldn't help the assault of memories that rushed to the front of his mind. It felt like it was lifetimes ago when he last saw her, and yet here she was, alive and well.

"How long has it been?" Martha asked.

"More than a thousand years," he answered.

"I like this face," Martha said. "It's very different, but it suits you. I almost didn't recognize you, but the eyes give you away."

"Doctor," Kate interrupted. "What do you need our help with?"

"Two of our friends have been taken by aliens," the Doctor answered.

Martha and Kate exchanged a worried look. "You must be very desperate to come to us," Kate said.

"These aliens are good. They know how to cover their tracks. I can't find them alone," the Doctor admitted.

Kate nodded solemnly and sat at her desk. "I'll run a quick scan of alien sightings within the past few months," she said. Her eyes flitted across the screen. "There's only been four, and they've all been non-hostile. Things have been relatively quiet." With a click of her mouse, the printer whirred to life. "I'm printing the list out for you. You're welcome to use our computers to take a look at the footage."

Martha retrieved the printed paper and handed it to the Doctor. "I can take the two of you down to a computer room, if you'd like," she offered.

The Doctor took the paper and glanced over the names. The list contained Vivocci, Hath, Silurians, and Judoon, neither of which were sighted anywhere in Britain. It felt as if his hearts dropped into his stomach at the unlikelihood of either of these aliens having Clara. Still, the Doctor decided it was worth looking into, but he hoped that he wasn't wasting time. The longer Clara and Molly were gone, the smaller there chances of finding them alive were.

"Yes, thank you," the Doctor replied.

"Do you think we've got a chance of finding the ones who took Clara?" John asked, speaking for the first time.

"Yes," the Doctor lied. "We'll find them soon. I know it." He smiled, hoping the fear in his eyes wouldn't give him away.

* * *

><p>Sherlock slumped down on Molly's couch, feeling defeated. He had spent hours searching both Clara's and Molly's flats, and he still couldn't identify which alien took them. Whatever they were, they were good. No, that was an understatement. They were experts.<p>

"It's like they were expecting me," Sherlock mused aloud.

"The Doctor is an excellent tracker too," Mycroft gently reminded him.

"Not like I am," Sherlock replied, shaking his head. "Are you positive we're dealing with aliens?"

"Yes," Mycroft answered.

"It looks like John trashed Clara's place looking for her. Even here, it's no clearer. Besides the busted door, there's no trace." Sherlock groaned as he ran his fingers through his hair. Things were looking grimmer by the second.

Absently, he rubbed at his sore wrist. It was just another reminder that the universe seemed to hate him. Ever since Moriarty's reappearance, he hadn't been able to catch a break.

Once again, he scanned the flat. Everything was in it's place. Sherlock squinted. There was a blue vase sitting on Molly's shelf, and from his position, he could see a tiny crack in it. "Well, that wasn't there before."

Mycroft's eyes shot over to the vase. "So there was a struggle," he said.

Sherlock bounded over to the shelf and examined the contents. "There's not as much dust," he concluded. "Whoever this was, they cleaned up their mess nicely."

"What do we do now?" Mycroft asked.

Sherlock grinned. "I need to make a phone call."

* * *

><p>The Doctor had been pouring over the videos for nearly an hour as John and Martha sat back and watched. "I think we can cross the Silurian pair off. They just looked lost, and they weren't here for very long before they climbed back into their ship. Besides, that was in Germany. Though I am curious as to how they got here in the first place."<p>

"So are we," Martha replied. "But like I said, they were non-hostile."

John sighed hopelessly. He knew the Doctor had been lying when he said that they would find Clara and Molly soon. For once, the Doctor was just as confused as John. Normally, he would have found that amusing, but in such a dire situation, it worried him to no end.

Not for the first time, John wished that Sherlock was there. Perhaps with his genius combined with the Doctor's, they would stand a chance at finding them. As it was now, they were searching for two needles in the proverbial haystack, except the haystack was infinite.

"The Judoon also, as it appears that they were only hunting down the Silurians," the Doctor added.

"What about the other two?" John asked.

"The two Vivocci were recovering a spaceship in Quebec. I suppose it's possible that they used that to sneak into London and kidnap out friends. They are our strongest suspects at the moment," the Doctor explained.

While it was indeed possible, it seemed highly unlikely to John. Judging by the fear in the Doctor's eyes, it seemed highly unlikely to him as well. Neither wanted to admit that they were grasping at straws. _I suppose straws is better than nothing, _John thought grimly.

"What about the Hath?" John asked.

"They touched down in Brazil, spied on the locals for a bit, then flew away. I would count them out."

"The Hath are generally peaceful anyways, so long as they are unprovoked," Martha added.

John's phone began ringing. With a heavy sigh, he pulled it out of his pocket. When he saw the number, he froze. "That's not possible," he said softly.

"What is it?" Martha asked curiously.

"It's my friend, only he's been dead for over a year now," John replied.

The Doctor whipped around fast to face John. "Sherlock?" he asked.

John nodded in response before answering the phone. "Hello?" he asked, holding his breath.

"John," the unmistakable voice on the other end responded.

"It really is you," John replied, amazed. "How?"

"Short version: not dead. Look, I know you have questions, and I'll explain everything. First, I need you and the Doctor to come pick me up. I'm at Molly's flat. I think I can help you find Clara and Molly."

"Bloody hell," John murmured, shaking his head with disbelief as the Doctor watched on in amazement. "Alright, we're coming."

There was a click from the other end, signaling that Sherlock had hung up again. John stared dumbly down at his phone. Of course, he had dreamed about this moment where he found at that his best friend wasn't dead, but he had lost all hope of it ever happening, and what he did imagine certainly wasn't anything like that phone call. Ecstatic joy rose through him, but it mingled with seething rage and bitter hurt. It was as if he was feeling everything at once. The overall feeling wasn't pleasant.

Martha was at the computer, moving files around. "I've put the videos onto a flash drive for you. It sounds as if you have to go somewhere."

"Yes," the Doctor agreed. He accepted the flash drive and pocketed it. "Where are we going, John?"

"Molly's flat," John answered.

As the pair stepped into the TARDIS, Martha raised her hand in farewell. "I hope you find your friends," she said.

The doors shut, and the Doctor set to work putting the coordinates in. "I don't believe it," John stated.

"Neither do I," the Doctor admitted.

"Do you think it's a trap?" John asked.

"It's possible," the Doctor replied. "Never hurts to be prepared."

John nodded in agreement. "Your friend is nice," he said, changing the subject. "Did you ever travel with her?"

"Yes," the Doctor answered. "That was two lifetimes ago."

The TARDIS lurched into the vortex, and John clung onto the rails for balance. He had no idea if he was heading towards his best friend or certain doom, and he had no idea what he was hoping for.


End file.
